Abstract Introduction The I-SPY2 neoadjuvant platform trial (NCT01042379) evaluates new therapies in high molecular risk breast cancer patients. From 2010-2022, 24 therapies were tested in 2117 patients. One-third of these patients had HER2-negative tumors with low expression of immune genes and no DNA repair deficiency (DRD) (HER2-/Immune-/DRD- subtype). These patients had very low pathologic complete response (pCR) rates (∼10% on average) across all treatment and control arms, whereas those patients with Immune, DRD, or HER2 targetable tumors had higher pCR rates (with the most successful treatments achieving pCR rates between 60-100%), associated with long-term survival benefit. Here, we focus on characterizing the biology of HER2-/Immune-/DRD- tumors, with the aim of identifying novel targetable vulnerabilities to increase treatment sensitivity in these treatment-resistant tumors. Methods We analyzed pre-treatment transcriptomic data of HR+HER2- (n = 889) and triple-negative (TN) (n = 739) patients across 20 treatment arms in I-SPY2 for enrichment of canonical metabolic, signaling, and regulatory pathways from the Molecular Signatures Database (n = 2274) including Hallmark, BioCarta, Reactome, and Pathway Interaction Database (PID) gene sets. We compared 1) HR+HER2-/Immune-/DRD- (n = 617) vs. other (Immune+ and/or DRD+) HR+HER2- tumors (n = 272) and 2) TN/Immune-/DRD- (n = 177) vs. other (Immune+ and/or DRD+) TN tumors (n = 562). Comparisons were made using Wilcoxon rank-sum tests with Benjamini-Hochberg adjustment. Results with adjusted p-values 0.05 were considered significant. Results Patients with HR+HER2-/Immune-/DRD- and TN-/Immune-/DRD- tumors had an overall pCR rate across all treatments, including chemoimmunotherapy, of 9% and 16%, respectively. Both subtypes had lower expression of the majority of canonical signaling pathway signatures, particularly of proliferation signatures, including those reflecting cell cycle checkpoints, Myc, and E2F targets, compared with other tumors, suggesting a quiescent-like phenotype. However, both HR+HER2-/Immune-/DRD- and TN-/Immune-/DRD- tumors had significantly enriched expression of signatures related to PI3K and FGFR signaling and fatty acid metabolism, which have previously been associated with treatment resistance. We identified subtype-specific signature enrichment with increased expression of WNT signaling and epigenetic modulators (e.g., HDAC) in HR+HER2-/Immune-/DRD- tumors, and enrichment of signatures reflecting coagulation events in TN/Immune-/DRD- tumors, which could potentially induce remodeling of the tumor microenvironment and/or mediate immune evasion, leading to resistance. Additional analysis of 87 epigenetic modulator genes in HR+HER2- tumors showed that 48 genes were significantly up- or downregulated in HR+HER2-/Immune-/DRD- compared with other tumors, suggesting that the quiescent-like phenotype may be driven by epigenetic silencing. Conclusion HR+HER2-/Immune-/DRD- and TN/Immune-/DRD- resistant tumors are characterized by low response to all therapies and low expression of many cancer-relevant biological pathways, including proliferation. Both had increased expression of PI3K and FGFR signaling signatures and fatty acid metabolism relative to more treatment-sensitive tumors that were Immune+ or DRD+. Moreover, receptor subtype-specific biology was identified. Our findings, which will be validated using RPPA functional signaling data from the rich I-SPY biomarker resource, suggest novel targetable vulnerabilities. These include pro-apoptotic and epigenetic targets, with already promising hits in drug screens with patient-derived organoids, supporting rapid translation to clinical trials. Citation Format: T. Bui, D. M. Wolf, R. W. Sayaman, C. Yau, A. M. Glas, J. Coppé, L. Brown Swigart, G. L. Hirst, P. R. Pohlmann, L. Pusztai, J. M. Rosenbluth, L. J. Esserman, E. F. Petricoin, L. J. Van 't Veer. Quiescent-like phenotype characterizes treatment-resistant early-stage HER2-negative breast cancers and suggests novel therapeutic targets; analysis of over 2000 patients from the I-SPY2 trial abstract. In: Proceedings of the San Antonio Breast Cancer Symposium 2025; 2025 Dec 9-12; San Antonio, TX. Philadelphia (PA): AACR; Clin Cancer Res 2026;32(4 Suppl):Abstract nr PS2-11-06.
Bui et al. (Tue,) studied this question.